Resolving deep animal phylogeny with irreversible and unrepeatable genomic changes

点击翻译按钮获取中文摘要

Resolving the animal tree of life is essential to understand the origin and evolution of complex traits such as muscles, guts, and a nervous system. Sequence-based phylogenomics has not met expectations- replacing old problems in animal phylogenetics with new ones. Different datasets and phylogenetic models routinely produce strongly supported but incompatible trees. A key driver of this is convergent evolution of the same nucleotide or amino acid character state at a given position in distantly related sequences by reverse or parallel substitutions. This is prevalent, given the few possible alternative nucleotide (4) or amino acid (20) states, and can produce incorrect trees. Despite substantial effort, adequate and tractable solutions to this and related problems continue to evade us, confounding understanding of animal evolution. An alternative is rare genomic changes, e.g. presence/absence of genes, indels, introns, gene clusters, protein domain architecture etc. Such complex characters are very unlikely to have evolved convergently and their presence/absence is a binary character uniting species. Despite the potential and growing use of such methods, it is already clear that like phylogenomics, they can be misled; character loss can be convergent and is indistinguishable from primary absence. To circumvent this, we will build computational tools for systematic genome-wide identification of a special class of rare genomic changes that employ 'irreversible', 'unrepeatable' characters. These characters are never absent and take two equally and highly complex conserved states-one ancestral (present in non-animals and some animals) and one derived (present in the remaining animals)-making reverse or parallel evolution vanishingly unlikely (e.g. gene adjacency relationships, 'conserved-but-different' genes). This will produce a new, confidently-resolved animal phylogeny allowing us to trace the history of animal trait evolution in ancient Precambrian oceans.